Hundreds of trees, plants and animals are to be moved from the runway site before the construction of the pounds 172m development, as part of an environmental package agreed by the airport authorities.
But Cheshire County Council said that two areas of the site have been destroyed by the protesters who were trying to prevent the runway. The airport campaign became a cause celebre and newspapers made a national celebrity of a previously unknown environmentalist nicknamed "Swampy".
The protesters denied yesterday that there was any mess. Jeff Gazzard, a spokesman for the campaigners, said: "Of course any outdoor protest will cause some damage, but nothing like on the scale the council are talking about. This just sounds like an excuse for the airport not to carry out its commitments and save money.
He added: "If they can show me this damage then I will certainly go to the site and clear it up."
Derek Bateman, chairman of the council's environment committee, said the land was littered with rotting food, razor blades, barbed wire and cesspits.
"Obviously all the wildlife has gone and the land itself has been damaged by tunnels and booby traps. The protesters were totally irresponsible in the way they treated the land and it means that we will not be able to relocate the trees, plants or animals," he said.
"It seems strange that these were people who said they wanted to protect the land."
About 100 protesters set up seven camps on the runway site and lived there until they were evicted by the building contractors earlier this year.
The clean-up of the site in the Bollin Valley, Cheshire, will continue until next month and then the relocation of the trees and undergrowth will begin.Reuse content